JPG won't flatten automatically

"Save As" now lists only the formats that support all the current properties of the file, thus preserving all your work. All other formats, with limited support, are now moved to "Save A Copy".

This was changed because the Save As jpeg function had already been broken for over a year on the Mac side, since Catalina. Saving over a jpeg resulted in a separate file with "-copy" appended. Apple did not want to change this, and there was no way for Adobe to work around it. The Save As jpeg function was terminally broken and finished, and had to be totally rewritten.

To be clear, saving a layered/16 bit file as jpeg saved out a copy the whole time. That is important to understand! The jpeg format does not allow 16 bit or layers. That fact was just hidden by Photoshop, but with Catalina it was no longer possible to hide.

Everybody should keep in mind that the direct save to jpeg, from 16 bit/layered files, was introduced in Photoshop CS5 in 2010. Prior to that, it was not possible at all to save directly to jpeg. First you had to remove every property in the file that wasn't supported in the jpeg specification. Only then could you save it. So this is nothing new - but this time you can use Save A Copy.

Platform parity has always been a sacred principle in Photoshop, so it had to be changed in the Windows version as well, even though it never was a problem on Windows.